EHV-1 TSS dynamics
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Canonic TSS dynamics
Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.8)... Done.## Bootstrap (r = 0.9)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.27)... Done.## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 2: 1 ORF4 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 3: 1 ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 4: 1 ORF7 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 5: 1 ORF9 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 6: 1 ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 7: 1 ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 8: 1 ORF20 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 9: 1 ORF21 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10: 1 ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11: 1 ORF31 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12: 1 ORF34 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 13: 1 ORF38 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 14: 1 ORF50 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 15: 1 ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 16: 1 ORF56 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 17: 1 ORF61 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 18: 1 ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 19: 1 NOIR_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 20: 1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 21: 1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 22: 1 ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 23: 1 NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 24: 2 ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25: 2 ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26: 2 ORF8 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 27: 2 ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 28: 2 ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 29: 2 ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 30: 2 ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 31: 2 ORF22 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 32: 2 ORF23 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 33: 2 ORF24 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 34: 2 ORF25 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 35: 2 ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 36: 2 ORF27 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 37: 2 ORF28 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 38: 2 ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 39: 2 ORF32 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 40: 2 ORF33 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 41: 2 ORF35.5 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 42: 2 ORF36 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 43: 2 ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 44: 2 ORF39 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 45: 2 CTO 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 46: 2 ORF40 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 47: 2 ORF42 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 48: 2 ORF43 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 49: 2 ORF44 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 50: 2 ORF46 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 51: 2 ORF49 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 52: 2 ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 53: 2 ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 54: 2 ORF58 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 55: 2 ORF59 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 56: 2 ORF62 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 57: 2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 58: 2 ORF68 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 59: 2 ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 60: 2 ORF74 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 61: 2 ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 62: 3 ORF6 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 63: 3 ORF70 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 64: 4 ORF12 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 65: 4 ORF13 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 66: 4 ORF15 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 67: 4 ORF16 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 68: 4 ORF35 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 69: 4 ORF41 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 70: 4 ORF45 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 71: 4 ORF48 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 72: 4 ORF52 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 73: 4 ORF54 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 74: 4 ORF57 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 75: 4 ORF60 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 76: 4 ORF71 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 77: 4 ORF72 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 78: 5 ORF64_1 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 79: 5 ORF75 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004376930 -1.8294074 0.9239714 0.05335458
## 2: 0.004376930 -1.8294074 0.9239714 0.05335458
## 3: 0.004376930 -1.8294074 0.9239714 0.05335458
## 4: 0.004376930 -1.8294074 0.9239714 0.05335458
## 5: 0.004376930 -1.8294074 0.9239714 0.05335458
## 6: 0.004376930 -1.8294074 0.9239714 0.05335458
## 7: 0.004376930 -1.8294074 0.9239714 0.05335458
## 8: 0.004376930 -1.8294074 0.9239714 0.05335458
## 9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.004376930 -1.8294074 0.9239714 0.05335458
## 13: 0.004376930 -1.8294074 0.9239714 0.05335458
## 14: 0.004376930 -1.8294074 0.9239714 0.05335458
## 15: 0.004376930 -1.8294074 0.9239714 0.05335458
## 16: 0.004376930 -1.8294074 0.9239714 0.05335458
## 17: 0.004376930 -1.8294074 0.9239714 0.05335458
## 18: 0.004376930 -1.8294074 0.9239714 0.05335458
## 19: 0.004376930 -1.8294074 0.9239714 0.05335458
## 20: 0.004376930 -1.8294074 0.9239714 0.05335458
## 21: 0.004376930 -1.8294074 0.9239714 0.05335458
## 22: 0.004376930 -1.8294074 0.9239714 0.05335458
## 23: 0.004376930 -1.8294074 0.9239714 0.05335458
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.005023951 -1.1447013 0.6730592 0.16333723
## 27: 0.005023951 -1.1447013 0.6730592 0.16333723
## 28: 0.005023951 -1.1447013 0.6730592 0.16333723
## 29: 0.005023951 -1.1447013 0.6730592 0.16333723
## 30: 0.005023951 -1.1447013 0.6730592 0.16333723
## 31: 0.005023951 -1.1447013 0.6730592 0.16333723
## 32: 0.005023951 -1.1447013 0.6730592 0.16333723
## 33: 0.005023951 -1.1447013 0.6730592 0.16333723
## 34: 0.005023951 -1.1447013 0.6730592 0.16333723
## 35: 0.005023951 -1.1447013 0.6730592 0.16333723
## 36: 0.005023951 -1.1447013 0.6730592 0.16333723
## 37: 0.005023951 -1.1447013 0.6730592 0.16333723
## 38: 0.005023951 -1.1447013 0.6730592 0.16333723
## 39: 0.005023951 -1.1447013 0.6730592 0.16333723
## 40: 0.005023951 -1.1447013 0.6730592 0.16333723
## 41: 0.005023951 -1.1447013 0.6730592 0.16333723
## 42: 0.005023951 -1.1447013 0.6730592 0.16333723
## 43: 0.005023951 -1.1447013 0.6730592 0.16333723
## 44: 0.005023951 -1.1447013 0.6730592 0.16333723
## 45: 0.005023951 -1.1447013 0.6730592 0.16333723
## 46: 0.005023951 -1.1447013 0.6730592 0.16333723
## 47: 0.005023951 -1.1447013 0.6730592 0.16333723
## 48: 0.005023951 -1.1447013 0.6730592 0.16333723
## 49: 0.005023951 -1.1447013 0.6730592 0.16333723
## 50: 0.005023951 -1.1447013 0.6730592 0.16333723
## 51: 0.005023951 -1.1447013 0.6730592 0.16333723
## 52: 0.005023951 -1.1447013 0.6730592 0.16333723
## 53: 0.005023951 -1.1447013 0.6730592 0.16333723
## 54: 0.005023951 -1.1447013 0.6730592 0.16333723
## 55: 0.005023951 -1.1447013 0.6730592 0.16333723
## 56: 0.005023951 -1.1447013 0.6730592 0.16333723
## 57: 0.005023951 -1.1447013 0.6730592 0.16333723
## 58: 0.005023951 -1.1447013 0.6730592 0.16333723
## 59: 0.005023951 -1.1447013 0.6730592 0.16333723
## 60: 0.005023951 -1.1447013 0.6730592 0.16333723
## 61: 0.005023951 -1.1447013 0.6730592 0.16333723
## 62: 0.004866876 -1.7084109 1.0563865 0.51628007
## 63: 0.004866876 -1.7084109 1.0563865 0.51628007
## 64: 0.004845179 -1.7779128 1.0925743 0.04880686
## 65: 0.004845179 -1.7779128 1.0925743 0.04880686
## 66: 0.004845179 -1.7779128 1.0925743 0.04880686
## 67: 0.004845179 -1.7779128 1.0925743 0.04880686
## 68: 0.004845179 -1.7779128 1.0925743 0.04880686
## 69: 0.004845179 -1.7779128 1.0925743 0.04880686
## 70: 0.004845179 -1.7779128 1.0925743 0.04880686
## 71: 0.004845179 -1.7779128 1.0925743 0.04880686
## 72: 0.004845179 -1.7779128 1.0925743 0.04880686
## 73: 0.004845179 -1.7779128 1.0925743 0.04880686
## 74: 0.004845179 -1.7779128 1.0925743 0.04880686
## 75: 0.004845179 -1.7779128 1.0925743 0.04880686
## 76: 0.004845179 -1.7779128 1.0925743 0.04880686
## 77: 0.004845179 -1.7779128 1.0925743 0.04880686
## 78: 0.004635436 -0.5796832 1.2128574 0.32603176
## 79: 0.004635436 -0.5796832 1.2128574 0.32603176
## se.bp v c pchi
## [1] "ORF67_1" "ORF32" "ORF58" "ORF33" "ORF35.5" "ORF25" "ORF27"
## [8] "ORF62"## [1] 8## character(0)## [1] 0Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 2: 1 ORF4 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 3: 1 ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 4: 1 ORF7 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 5: 1 ORF9 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 6: 1 ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 7: 1 ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 8: 1 ORF20 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 9: 1 ORF21 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10: 1 ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11: 1 ORF31 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12: 1 ORF34 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 13: 1 ORF38 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 14: 1 ORF50 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 15: 1 ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 16: 1 ORF56 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 17: 1 ORF61 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 18: 1 ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 19: 1 NOIR_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 20: 1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 21: 1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 22: 1 ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 23: 1 NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 24: 2 ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25: 2 ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26: 2 ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 27: 2 ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 28: 2 ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 29: 2 ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 30: 2 ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 31: 2 ORF28 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 32: 2 ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 33: 2 ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 34: 2 ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 35: 2 ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 36: 2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 37: 2 ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 38: 2 ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 39: 3 ORF6 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 40: 3 ORF70 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 41: 4 ORF8 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 42: 4 ORF22 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 43: 4 ORF23 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 44: 4 ORF24 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 45: 4 ORF25 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 46: 4 ORF27 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 47: 4 ORF32 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 48: 4 ORF33 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 49: 4 ORF35.5 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 50: 4 ORF36 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 51: 4 ORF39 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 52: 4 CTO 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 53: 4 ORF40 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 54: 4 ORF42 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 55: 4 ORF43 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 56: 4 ORF44 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 57: 4 ORF46 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 58: 4 ORF49 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 59: 4 ORF58 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 60: 4 ORF59 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 61: 4 ORF62 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 62: 4 ORF68 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 63: 4 ORF74 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 64: 5 ORF12 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 65: 5 ORF13 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 66: 5 ORF15 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 67: 5 ORF16 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 68: 5 ORF35 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 69: 5 ORF41 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 70: 5 ORF45 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 71: 5 ORF48 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 72: 5 ORF52 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 73: 5 ORF54 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 74: 5 ORF57 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 75: 5 ORF60 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 76: 5 ORF71 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 77: 5 ORF72 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 78: 6 ORF64_1 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 79: 6 ORF75 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004376930 -1.8294074 0.9239714 0.05335458
## 2: 0.004376930 -1.8294074 0.9239714 0.05335458
## 3: 0.004376930 -1.8294074 0.9239714 0.05335458
## 4: 0.004376930 -1.8294074 0.9239714 0.05335458
## 5: 0.004376930 -1.8294074 0.9239714 0.05335458
## 6: 0.004376930 -1.8294074 0.9239714 0.05335458
## 7: 0.004376930 -1.8294074 0.9239714 0.05335458
## 8: 0.004376930 -1.8294074 0.9239714 0.05335458
## 9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.004376930 -1.8294074 0.9239714 0.05335458
## 13: 0.004376930 -1.8294074 0.9239714 0.05335458
## 14: 0.004376930 -1.8294074 0.9239714 0.05335458
## 15: 0.004376930 -1.8294074 0.9239714 0.05335458
## 16: 0.004376930 -1.8294074 0.9239714 0.05335458
## 17: 0.004376930 -1.8294074 0.9239714 0.05335458
## 18: 0.004376930 -1.8294074 0.9239714 0.05335458
## 19: 0.004376930 -1.8294074 0.9239714 0.05335458
## 20: 0.004376930 -1.8294074 0.9239714 0.05335458
## 21: 0.004376930 -1.8294074 0.9239714 0.05335458
## 22: 0.004376930 -1.8294074 0.9239714 0.05335458
## 23: 0.004376930 -1.8294074 0.9239714 0.05335458
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.005023951 -1.1447013 0.6730592 0.16333723
## 27: 0.005023951 -1.1447013 0.6730592 0.16333723
## 28: 0.005023951 -1.1447013 0.6730592 0.16333723
## 29: 0.005023951 -1.1447013 0.6730592 0.16333723
## 30: 0.005023951 -1.1447013 0.6730592 0.16333723
## 31: 0.005023951 -1.1447013 0.6730592 0.16333723
## 32: 0.005023951 -1.1447013 0.6730592 0.16333723
## 33: 0.005023951 -1.1447013 0.6730592 0.16333723
## 34: 0.005023951 -1.1447013 0.6730592 0.16333723
## 35: 0.005023951 -1.1447013 0.6730592 0.16333723
## 36: 0.005023951 -1.1447013 0.6730592 0.16333723
## 37: 0.005023951 -1.1447013 0.6730592 0.16333723
## 38: 0.005023951 -1.1447013 0.6730592 0.16333723
## 39: 0.004866876 -1.7084109 1.0563865 0.51628007
## 40: 0.004866876 -1.7084109 1.0563865 0.51628007
## 41: 0.004845179 -1.7779128 1.0925743 0.04880686
## 42: 0.004845179 -1.7779128 1.0925743 0.04880686
## 43: 0.004845179 -1.7779128 1.0925743 0.04880686
## 44: 0.004845179 -1.7779128 1.0925743 0.04880686
## 45: 0.004845179 -1.7779128 1.0925743 0.04880686
## 46: 0.004845179 -1.7779128 1.0925743 0.04880686
## 47: 0.004845179 -1.7779128 1.0925743 0.04880686
## 48: 0.004845179 -1.7779128 1.0925743 0.04880686
## 49: 0.004845179 -1.7779128 1.0925743 0.04880686
## 50: 0.004845179 -1.7779128 1.0925743 0.04880686
## 51: 0.004845179 -1.7779128 1.0925743 0.04880686
## 52: 0.004845179 -1.7779128 1.0925743 0.04880686
## 53: 0.004845179 -1.7779128 1.0925743 0.04880686
## 54: 0.004845179 -1.7779128 1.0925743 0.04880686
## 55: 0.004845179 -1.7779128 1.0925743 0.04880686
## 56: 0.004845179 -1.7779128 1.0925743 0.04880686
## 57: 0.004845179 -1.7779128 1.0925743 0.04880686
## 58: 0.004845179 -1.7779128 1.0925743 0.04880686
## 59: 0.004845179 -1.7779128 1.0925743 0.04880686
## 60: 0.004845179 -1.7779128 1.0925743 0.04880686
## 61: 0.004845179 -1.7779128 1.0925743 0.04880686
## 62: 0.004845179 -1.7779128 1.0925743 0.04880686
## 63: 0.004845179 -1.7779128 1.0925743 0.04880686
## 64: 0.004635436 -0.5796832 1.2128574 0.32603176
## 65: 0.004635436 -0.5796832 1.2128574 0.32603176
## 66: 0.004635436 -0.5796832 1.2128574 0.32603176
## 67: 0.004635436 -0.5796832 1.2128574 0.32603176
## 68: 0.004635436 -0.5796832 1.2128574 0.32603176
## 69: 0.004635436 -0.5796832 1.2128574 0.32603176
## 70: 0.004635436 -0.5796832 1.2128574 0.32603176
## 71: 0.004635436 -0.5796832 1.2128574 0.32603176
## 72: 0.004635436 -0.5796832 1.2128574 0.32603176
## 73: 0.004635436 -0.5796832 1.2128574 0.32603176
## 74: 0.004635436 -0.5796832 1.2128574 0.32603176
## 75: 0.004635436 -0.5796832 1.2128574 0.32603176
## 76: 0.004635436 -0.5796832 1.2128574 0.32603176
## 77: 0.004635436 -0.5796832 1.2128574 0.32603176
## 78: 0.005225222 -1.2149856 0.9031625 0.82402823
## 79: 0.005225222 -1.2149856 0.9031625 0.82402823
## se.bp v c pchi
## [1] "ORF67_1" "ORF9" "ORF73" "ORF32" "ORF62" "ORF45"## [1] 6## character(0)## [1] 0Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 2: 1 ORF4 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 3: 1 ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 4: 1 ORF7 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 5: 1 ORF9 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 6: 1 ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 7: 1 ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 8: 1 ORF20 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 9: 1 ORF21 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10: 1 ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11: 1 ORF31 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12: 1 ORF34 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 13: 1 ORF38 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 14: 1 ORF50 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 15: 1 ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 16: 1 ORF56 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 17: 1 ORF61 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 18: 1 ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 19: 1 NOIR_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 20: 1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 21: 1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 22: 1 ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 23: 1 NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 24: 2 ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25: 2 ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26: 2 ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 27: 2 ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 28: 2 ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 29: 2 ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 30: 2 ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 31: 2 ORF28 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 32: 2 ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 33: 2 ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 34: 2 ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 35: 2 ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 36: 2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 37: 2 ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 38: 2 ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 39: 3 ORF6 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 40: 3 ORF70 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 41: 4 ORF8 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 42: 4 ORF22 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 43: 4 ORF23 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 44: 4 ORF24 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 45: 4 ORF25 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 46: 4 ORF27 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 47: 4 ORF32 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 48: 4 ORF33 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 49: 4 ORF35.5 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 50: 4 ORF36 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 51: 4 ORF39 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 52: 4 CTO 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 53: 4 ORF40 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 54: 4 ORF42 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 55: 4 ORF43 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 56: 4 ORF44 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 57: 4 ORF46 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 58: 4 ORF49 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 59: 4 ORF58 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 60: 4 ORF59 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 61: 4 ORF62 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 62: 4 ORF68 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 63: 4 ORF74 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 64: 5 ORF12 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 65: 5 ORF13 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 66: 5 ORF15 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 67: 5 ORF16 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 68: 5 ORF35 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 69: 5 ORF41 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 70: 5 ORF48 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 71: 5 ORF52 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 72: 5 ORF54 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 73: 5 ORF57 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 74: 5 ORF60 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 75: 5 ORF71 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 76: 5 ORF72 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 77: 6 ORF45 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 78: 7 ORF64_1 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 79: 7 ORF75 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004376930 -1.8294074 0.9239714 0.05335458
## 2: 0.004376930 -1.8294074 0.9239714 0.05335458
## 3: 0.004376930 -1.8294074 0.9239714 0.05335458
## 4: 0.004376930 -1.8294074 0.9239714 0.05335458
## 5: 0.004376930 -1.8294074 0.9239714 0.05335458
## 6: 0.004376930 -1.8294074 0.9239714 0.05335458
## 7: 0.004376930 -1.8294074 0.9239714 0.05335458
## 8: 0.004376930 -1.8294074 0.9239714 0.05335458
## 9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.004376930 -1.8294074 0.9239714 0.05335458
## 13: 0.004376930 -1.8294074 0.9239714 0.05335458
## 14: 0.004376930 -1.8294074 0.9239714 0.05335458
## 15: 0.004376930 -1.8294074 0.9239714 0.05335458
## 16: 0.004376930 -1.8294074 0.9239714 0.05335458
## 17: 0.004376930 -1.8294074 0.9239714 0.05335458
## 18: 0.004376930 -1.8294074 0.9239714 0.05335458
## 19: 0.004376930 -1.8294074 0.9239714 0.05335458
## 20: 0.004376930 -1.8294074 0.9239714 0.05335458
## 21: 0.004376930 -1.8294074 0.9239714 0.05335458
## 22: 0.004376930 -1.8294074 0.9239714 0.05335458
## 23: 0.004376930 -1.8294074 0.9239714 0.05335458
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.005023951 -1.1447013 0.6730592 0.16333723
## 27: 0.005023951 -1.1447013 0.6730592 0.16333723
## 28: 0.005023951 -1.1447013 0.6730592 0.16333723
## 29: 0.005023951 -1.1447013 0.6730592 0.16333723
## 30: 0.005023951 -1.1447013 0.6730592 0.16333723
## 31: 0.005023951 -1.1447013 0.6730592 0.16333723
## 32: 0.005023951 -1.1447013 0.6730592 0.16333723
## 33: 0.005023951 -1.1447013 0.6730592 0.16333723
## 34: 0.005023951 -1.1447013 0.6730592 0.16333723
## 35: 0.005023951 -1.1447013 0.6730592 0.16333723
## 36: 0.005023951 -1.1447013 0.6730592 0.16333723
## 37: 0.005023951 -1.1447013 0.6730592 0.16333723
## 38: 0.005023951 -1.1447013 0.6730592 0.16333723
## 39: 0.004866876 -1.7084109 1.0563865 0.51628007
## 40: 0.004866876 -1.7084109 1.0563865 0.51628007
## 41: 0.004845179 -1.7779128 1.0925743 0.04880686
## 42: 0.004845179 -1.7779128 1.0925743 0.04880686
## 43: 0.004845179 -1.7779128 1.0925743 0.04880686
## 44: 0.004845179 -1.7779128 1.0925743 0.04880686
## 45: 0.004845179 -1.7779128 1.0925743 0.04880686
## 46: 0.004845179 -1.7779128 1.0925743 0.04880686
## 47: 0.004845179 -1.7779128 1.0925743 0.04880686
## 48: 0.004845179 -1.7779128 1.0925743 0.04880686
## 49: 0.004845179 -1.7779128 1.0925743 0.04880686
## 50: 0.004845179 -1.7779128 1.0925743 0.04880686
## 51: 0.004845179 -1.7779128 1.0925743 0.04880686
## 52: 0.004845179 -1.7779128 1.0925743 0.04880686
## 53: 0.004845179 -1.7779128 1.0925743 0.04880686
## 54: 0.004845179 -1.7779128 1.0925743 0.04880686
## 55: 0.004845179 -1.7779128 1.0925743 0.04880686
## 56: 0.004845179 -1.7779128 1.0925743 0.04880686
## 57: 0.004845179 -1.7779128 1.0925743 0.04880686
## 58: 0.004845179 -1.7779128 1.0925743 0.04880686
## 59: 0.004845179 -1.7779128 1.0925743 0.04880686
## 60: 0.004845179 -1.7779128 1.0925743 0.04880686
## 61: 0.004845179 -1.7779128 1.0925743 0.04880686
## 62: 0.004845179 -1.7779128 1.0925743 0.04880686
## 63: 0.004845179 -1.7779128 1.0925743 0.04880686
## 64: 0.004635436 -0.5796832 1.2128574 0.32603176
## 65: 0.004635436 -0.5796832 1.2128574 0.32603176
## 66: 0.004635436 -0.5796832 1.2128574 0.32603176
## 67: 0.004635436 -0.5796832 1.2128574 0.32603176
## 68: 0.004635436 -0.5796832 1.2128574 0.32603176
## 69: 0.004635436 -0.5796832 1.2128574 0.32603176
## 70: 0.004635436 -0.5796832 1.2128574 0.32603176
## 71: 0.004635436 -0.5796832 1.2128574 0.32603176
## 72: 0.004635436 -0.5796832 1.2128574 0.32603176
## 73: 0.004635436 -0.5796832 1.2128574 0.32603176
## 74: 0.004635436 -0.5796832 1.2128574 0.32603176
## 75: 0.004635436 -0.5796832 1.2128574 0.32603176
## 76: 0.004635436 -0.5796832 1.2128574 0.32603176
## 77: 0.005225222 -1.2149856 0.9031625 0.82402823
## 78: 0.004968046 -1.4394451 0.8949157 0.71371866
## 79: 0.004968046 -1.4394451 0.8949157 0.71371866
## se.bp v c pchi
## [1] "ORF67_1" "ORF9" "ORF73" "ORF27" "ORF32" "ORF62"## [1] 6## character(0)## [1] 0Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 2: 1 ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 3: 1 ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 4: 1 ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 5: 1 ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 6: 1 ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 7: 1 ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 8: 1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 9: 1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10: 1 ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11: 1 NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12: 2 ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 13: 2 ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 14: 2 ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 15: 2 ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 16: 2 ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 17: 2 ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 18: 2 ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 19: 2 ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 20: 2 ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 21: 2 ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 22: 2 ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 23: 2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 24: 2 ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25: 2 ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26: 3 ORF4 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 27: 3 ORF7 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 28: 3 ORF9 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 29: 3 ORF20 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 30: 3 ORF21 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 31: 3 ORF31 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 32: 3 ORF34 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 33: 3 ORF38 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 34: 3 ORF50 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 35: 3 ORF56 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 36: 3 ORF61 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 37: 3 NOIR_1 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 38: 4 ORF6 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 39: 4 ORF70 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 40: 5 ORF8 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 41: 5 ORF22 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 42: 5 ORF23 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 43: 5 ORF24 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 44: 5 ORF25 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 45: 5 ORF33 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 46: 5 ORF35.5 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 47: 5 ORF36 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 48: 5 ORF39 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 49: 5 CTO 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 50: 5 ORF40 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 51: 5 ORF42 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 52: 5 ORF43 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 53: 5 ORF44 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 54: 5 ORF46 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 55: 5 ORF49 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 56: 5 ORF58 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 57: 5 ORF62 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 58: 5 ORF68 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 59: 5 ORF74 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 60: 6 ORF12 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 61: 6 ORF13 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 62: 6 ORF15 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 63: 6 ORF16 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 64: 6 ORF35 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 65: 6 ORF41 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 66: 6 ORF48 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 67: 6 ORF52 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 68: 6 ORF54 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 69: 6 ORF57 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 70: 6 ORF60 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 71: 6 ORF71 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 72: 6 ORF72 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 73: 7 ORF27 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 74: 7 ORF32 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 75: 7 ORF59 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 76: 8 ORF28 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 77: 9 ORF45 0.5315416 0.9101709 0.3441776 0.044014262 0.0134541621
## 78: 10 ORF64_1 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
## 79: 10 ORF75 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004376930 -1.8294074 0.9239714 0.05335458
## 2: 0.004376930 -1.8294074 0.9239714 0.05335458
## 3: 0.004376930 -1.8294074 0.9239714 0.05335458
## 4: 0.004376930 -1.8294074 0.9239714 0.05335458
## 5: 0.004376930 -1.8294074 0.9239714 0.05335458
## 6: 0.004376930 -1.8294074 0.9239714 0.05335458
## 7: 0.004376930 -1.8294074 0.9239714 0.05335458
## 8: 0.004376930 -1.8294074 0.9239714 0.05335458
## 9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.005023951 -1.1447013 0.6730592 0.16333723
## 13: 0.005023951 -1.1447013 0.6730592 0.16333723
## 14: 0.005023951 -1.1447013 0.6730592 0.16333723
## 15: 0.005023951 -1.1447013 0.6730592 0.16333723
## 16: 0.005023951 -1.1447013 0.6730592 0.16333723
## 17: 0.005023951 -1.1447013 0.6730592 0.16333723
## 18: 0.005023951 -1.1447013 0.6730592 0.16333723
## 19: 0.005023951 -1.1447013 0.6730592 0.16333723
## 20: 0.005023951 -1.1447013 0.6730592 0.16333723
## 21: 0.005023951 -1.1447013 0.6730592 0.16333723
## 22: 0.005023951 -1.1447013 0.6730592 0.16333723
## 23: 0.005023951 -1.1447013 0.6730592 0.16333723
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.004866876 -1.7084109 1.0563865 0.51628007
## 27: 0.004866876 -1.7084109 1.0563865 0.51628007
## 28: 0.004866876 -1.7084109 1.0563865 0.51628007
## 29: 0.004866876 -1.7084109 1.0563865 0.51628007
## 30: 0.004866876 -1.7084109 1.0563865 0.51628007
## 31: 0.004866876 -1.7084109 1.0563865 0.51628007
## 32: 0.004866876 -1.7084109 1.0563865 0.51628007
## 33: 0.004866876 -1.7084109 1.0563865 0.51628007
## 34: 0.004866876 -1.7084109 1.0563865 0.51628007
## 35: 0.004866876 -1.7084109 1.0563865 0.51628007
## 36: 0.004866876 -1.7084109 1.0563865 0.51628007
## 37: 0.004866876 -1.7084109 1.0563865 0.51628007
## 38: 0.004845179 -1.7779128 1.0925743 0.04880686
## 39: 0.004845179 -1.7779128 1.0925743 0.04880686
## 40: 0.004635436 -0.5796832 1.2128574 0.32603176
## 41: 0.004635436 -0.5796832 1.2128574 0.32603176
## 42: 0.004635436 -0.5796832 1.2128574 0.32603176
## 43: 0.004635436 -0.5796832 1.2128574 0.32603176
## 44: 0.004635436 -0.5796832 1.2128574 0.32603176
## 45: 0.004635436 -0.5796832 1.2128574 0.32603176
## 46: 0.004635436 -0.5796832 1.2128574 0.32603176
## 47: 0.004635436 -0.5796832 1.2128574 0.32603176
## 48: 0.004635436 -0.5796832 1.2128574 0.32603176
## 49: 0.004635436 -0.5796832 1.2128574 0.32603176
## 50: 0.004635436 -0.5796832 1.2128574 0.32603176
## 51: 0.004635436 -0.5796832 1.2128574 0.32603176
## 52: 0.004635436 -0.5796832 1.2128574 0.32603176
## 53: 0.004635436 -0.5796832 1.2128574 0.32603176
## 54: 0.004635436 -0.5796832 1.2128574 0.32603176
## 55: 0.004635436 -0.5796832 1.2128574 0.32603176
## 56: 0.004635436 -0.5796832 1.2128574 0.32603176
## 57: 0.004635436 -0.5796832 1.2128574 0.32603176
## 58: 0.004635436 -0.5796832 1.2128574 0.32603176
## 59: 0.004635436 -0.5796832 1.2128574 0.32603176
## 60: 0.005225222 -1.2149856 0.9031625 0.82402823
## 61: 0.005225222 -1.2149856 0.9031625 0.82402823
## 62: 0.005225222 -1.2149856 0.9031625 0.82402823
## 63: 0.005225222 -1.2149856 0.9031625 0.82402823
## 64: 0.005225222 -1.2149856 0.9031625 0.82402823
## 65: 0.005225222 -1.2149856 0.9031625 0.82402823
## 66: 0.005225222 -1.2149856 0.9031625 0.82402823
## 67: 0.005225222 -1.2149856 0.9031625 0.82402823
## 68: 0.005225222 -1.2149856 0.9031625 0.82402823
## 69: 0.005225222 -1.2149856 0.9031625 0.82402823
## 70: 0.005225222 -1.2149856 0.9031625 0.82402823
## 71: 0.005225222 -1.2149856 0.9031625 0.82402823
## 72: 0.005225222 -1.2149856 0.9031625 0.82402823
## 73: 0.004968046 -1.4394451 0.8949157 0.71371866
## 74: 0.004968046 -1.4394451 0.8949157 0.71371866
## 75: 0.004968046 -1.4394451 0.8949157 0.71371866
## 76: 0.005268284 -0.8383279 0.9900376 0.17121312
## 77: 0.005000790 -0.4703599 0.8714482 0.43210675
## 78: 0.005399375 -1.4831325 1.4450987 0.32741114
## 79: 0.005399375 -1.4831325 1.4450987 0.32741114
## se.bp v c pchi
## [1] "ORF55" "ORF73" "ORF62" "ORF27" "ORF32" "ORF59"## [1] 6## [1] "ORF45"## [1] 1Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 2: 1 ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 3: 1 ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 4: 1 ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 5: 1 ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 6: 1 ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 7: 1 ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 8: 1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 9: 1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10: 1 ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11: 1 NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12: 2 ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 13: 2 ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 14: 2 ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 15: 2 ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 16: 2 ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 17: 2 ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 18: 2 ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 19: 2 ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 20: 2 ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 21: 2 ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 22: 2 ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 23: 2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 24: 2 ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25: 2 ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26: 3 ORF4 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 27: 3 ORF9 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 28: 3 ORF20 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 29: 3 ORF21 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 30: 3 ORF31 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 31: 3 ORF34 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 32: 3 ORF38 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 33: 3 ORF50 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 34: 3 ORF61 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 35: 4 ORF6 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 36: 4 ORF70 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 37: 5 ORF7 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 38: 5 ORF56 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 39: 5 NOIR_1 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 40: 6 ORF8 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 41: 6 ORF22 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 42: 6 ORF23 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 43: 6 ORF24 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 44: 6 ORF25 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 45: 6 ORF33 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 46: 6 ORF35.5 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 47: 6 ORF36 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 48: 6 ORF39 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 49: 6 CTO 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 50: 6 ORF40 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 51: 6 ORF42 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 52: 6 ORF43 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 53: 6 ORF44 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 54: 6 ORF46 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 55: 6 ORF49 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 56: 6 ORF58 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 57: 6 ORF62 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 58: 6 ORF68 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 59: 6 ORF74 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 60: 7 ORF12 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 61: 7 ORF13 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 62: 7 ORF15 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 63: 7 ORF16 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 64: 7 ORF35 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 65: 7 ORF41 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 66: 7 ORF48 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 67: 7 ORF52 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 68: 7 ORF54 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 69: 7 ORF57 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 70: 7 ORF60 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 71: 7 ORF71 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 72: 7 ORF72 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 73: 8 ORF27 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 74: 8 ORF59 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 75: 9 ORF28 0.5315416 0.9101709 0.3441776 0.044014262 0.0134541621
## 76: 10 ORF32 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
## 77: 11 ORF45 0.6926659 0.9668711 0.2610828 0.038775743 0.0066333119
## 78: 12 ORF64_1 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
## 79: 12 ORF75 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004376930 -1.8294074 0.9239714 0.05335458
## 2: 0.004376930 -1.8294074 0.9239714 0.05335458
## 3: 0.004376930 -1.8294074 0.9239714 0.05335458
## 4: 0.004376930 -1.8294074 0.9239714 0.05335458
## 5: 0.004376930 -1.8294074 0.9239714 0.05335458
## 6: 0.004376930 -1.8294074 0.9239714 0.05335458
## 7: 0.004376930 -1.8294074 0.9239714 0.05335458
## 8: 0.004376930 -1.8294074 0.9239714 0.05335458
## 9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.005023951 -1.1447013 0.6730592 0.16333723
## 13: 0.005023951 -1.1447013 0.6730592 0.16333723
## 14: 0.005023951 -1.1447013 0.6730592 0.16333723
## 15: 0.005023951 -1.1447013 0.6730592 0.16333723
## 16: 0.005023951 -1.1447013 0.6730592 0.16333723
## 17: 0.005023951 -1.1447013 0.6730592 0.16333723
## 18: 0.005023951 -1.1447013 0.6730592 0.16333723
## 19: 0.005023951 -1.1447013 0.6730592 0.16333723
## 20: 0.005023951 -1.1447013 0.6730592 0.16333723
## 21: 0.005023951 -1.1447013 0.6730592 0.16333723
## 22: 0.005023951 -1.1447013 0.6730592 0.16333723
## 23: 0.005023951 -1.1447013 0.6730592 0.16333723
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.004866876 -1.7084109 1.0563865 0.51628007
## 27: 0.004866876 -1.7084109 1.0563865 0.51628007
## 28: 0.004866876 -1.7084109 1.0563865 0.51628007
## 29: 0.004866876 -1.7084109 1.0563865 0.51628007
## 30: 0.004866876 -1.7084109 1.0563865 0.51628007
## 31: 0.004866876 -1.7084109 1.0563865 0.51628007
## 32: 0.004866876 -1.7084109 1.0563865 0.51628007
## 33: 0.004866876 -1.7084109 1.0563865 0.51628007
## 34: 0.004866876 -1.7084109 1.0563865 0.51628007
## 35: 0.004845179 -1.7779128 1.0925743 0.04880686
## 36: 0.004845179 -1.7779128 1.0925743 0.04880686
## 37: 0.004635436 -0.5796832 1.2128574 0.32603176
## 38: 0.004635436 -0.5796832 1.2128574 0.32603176
## 39: 0.004635436 -0.5796832 1.2128574 0.32603176
## 40: 0.005225222 -1.2149856 0.9031625 0.82402823
## 41: 0.005225222 -1.2149856 0.9031625 0.82402823
## 42: 0.005225222 -1.2149856 0.9031625 0.82402823
## 43: 0.005225222 -1.2149856 0.9031625 0.82402823
## 44: 0.005225222 -1.2149856 0.9031625 0.82402823
## 45: 0.005225222 -1.2149856 0.9031625 0.82402823
## 46: 0.005225222 -1.2149856 0.9031625 0.82402823
## 47: 0.005225222 -1.2149856 0.9031625 0.82402823
## 48: 0.005225222 -1.2149856 0.9031625 0.82402823
## 49: 0.005225222 -1.2149856 0.9031625 0.82402823
## 50: 0.005225222 -1.2149856 0.9031625 0.82402823
## 51: 0.005225222 -1.2149856 0.9031625 0.82402823
## 52: 0.005225222 -1.2149856 0.9031625 0.82402823
## 53: 0.005225222 -1.2149856 0.9031625 0.82402823
## 54: 0.005225222 -1.2149856 0.9031625 0.82402823
## 55: 0.005225222 -1.2149856 0.9031625 0.82402823
## 56: 0.005225222 -1.2149856 0.9031625 0.82402823
## 57: 0.005225222 -1.2149856 0.9031625 0.82402823
## 58: 0.005225222 -1.2149856 0.9031625 0.82402823
## 59: 0.005225222 -1.2149856 0.9031625 0.82402823
## 60: 0.004968046 -1.4394451 0.8949157 0.71371866
## 61: 0.004968046 -1.4394451 0.8949157 0.71371866
## 62: 0.004968046 -1.4394451 0.8949157 0.71371866
## 63: 0.004968046 -1.4394451 0.8949157 0.71371866
## 64: 0.004968046 -1.4394451 0.8949157 0.71371866
## 65: 0.004968046 -1.4394451 0.8949157 0.71371866
## 66: 0.004968046 -1.4394451 0.8949157 0.71371866
## 67: 0.004968046 -1.4394451 0.8949157 0.71371866
## 68: 0.004968046 -1.4394451 0.8949157 0.71371866
## 69: 0.004968046 -1.4394451 0.8949157 0.71371866
## 70: 0.004968046 -1.4394451 0.8949157 0.71371866
## 71: 0.004968046 -1.4394451 0.8949157 0.71371866
## 72: 0.004968046 -1.4394451 0.8949157 0.71371866
## 73: 0.005268284 -0.8383279 0.9900376 0.17121312
## 74: 0.005268284 -0.8383279 0.9900376 0.17121312
## 75: 0.005000790 -0.4703599 0.8714482 0.43210675
## 76: 0.005399375 -1.4831325 1.4450987 0.32741114
## 77: 0.004627003 -0.5983324 1.2383432 0.10503633
## 78: 0.004794327 -0.4644118 1.0058356 0.11286204
## 79: 0.004794327 -0.4644118 1.0058356 0.11286204
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF55" "ORF73" "ORF62"## [1] 5## [1] "ORF28" "ORF64_1" "ORF75"## [1] 3Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 2: 1 ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 3: 1 ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 4: 1 ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 5: 1 ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 6: 1 ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 7: 1 ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 8: 1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 9: 1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10: 1 ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11: 1 NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12: 2 ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 13: 2 ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 14: 2 ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 15: 2 ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 16: 2 ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 17: 2 ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 18: 2 ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 19: 2 ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 20: 2 ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 21: 2 ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 22: 2 ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 23: 2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 24: 2 ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25: 2 ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26: 3 ORF4 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 27: 3 ORF9 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 28: 3 ORF20 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 29: 3 ORF21 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 30: 3 ORF31 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 31: 3 ORF34 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 32: 3 ORF38 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 33: 3 ORF50 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 34: 3 ORF61 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 35: 4 ORF6 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 36: 4 ORF70 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 37: 5 ORF7 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 38: 5 ORF56 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 39: 5 NOIR_1 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 40: 6 ORF8 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 41: 6 ORF22 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 42: 6 ORF23 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 43: 6 ORF24 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 44: 6 ORF25 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 45: 6 ORF33 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 46: 6 ORF35.5 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 47: 6 ORF36 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 48: 6 ORF39 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 49: 6 CTO 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 50: 6 ORF40 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 51: 6 ORF42 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 52: 6 ORF43 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 53: 6 ORF44 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 54: 6 ORF46 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 55: 6 ORF49 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 56: 6 ORF58 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 57: 6 ORF62 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 58: 6 ORF68 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 59: 6 ORF74 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 60: 7 ORF12 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 61: 7 ORF13 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 62: 7 ORF15 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 63: 7 ORF16 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 64: 7 ORF35 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 65: 7 ORF41 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 66: 7 ORF48 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 67: 7 ORF52 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 68: 7 ORF54 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 69: 7 ORF57 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 70: 7 ORF60 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 71: 7 ORF71 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 72: 7 ORF72 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 73: 8 ORF27 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 74: 8 ORF59 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 75: 9 ORF28 0.5315416 0.9101709 0.3441776 0.044014262 0.0134541621
## 76: 10 ORF32 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
## 77: 11 ORF45 0.6926659 0.9668711 0.2610828 0.038775743 0.0066333119
## 78: 12 ORF64_1 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
## 79: 12 ORF75 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004376930 -1.8294074 0.9239714 0.05335458
## 2: 0.004376930 -1.8294074 0.9239714 0.05335458
## 3: 0.004376930 -1.8294074 0.9239714 0.05335458
## 4: 0.004376930 -1.8294074 0.9239714 0.05335458
## 5: 0.004376930 -1.8294074 0.9239714 0.05335458
## 6: 0.004376930 -1.8294074 0.9239714 0.05335458
## 7: 0.004376930 -1.8294074 0.9239714 0.05335458
## 8: 0.004376930 -1.8294074 0.9239714 0.05335458
## 9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.005023951 -1.1447013 0.6730592 0.16333723
## 13: 0.005023951 -1.1447013 0.6730592 0.16333723
## 14: 0.005023951 -1.1447013 0.6730592 0.16333723
## 15: 0.005023951 -1.1447013 0.6730592 0.16333723
## 16: 0.005023951 -1.1447013 0.6730592 0.16333723
## 17: 0.005023951 -1.1447013 0.6730592 0.16333723
## 18: 0.005023951 -1.1447013 0.6730592 0.16333723
## 19: 0.005023951 -1.1447013 0.6730592 0.16333723
## 20: 0.005023951 -1.1447013 0.6730592 0.16333723
## 21: 0.005023951 -1.1447013 0.6730592 0.16333723
## 22: 0.005023951 -1.1447013 0.6730592 0.16333723
## 23: 0.005023951 -1.1447013 0.6730592 0.16333723
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.004866876 -1.7084109 1.0563865 0.51628007
## 27: 0.004866876 -1.7084109 1.0563865 0.51628007
## 28: 0.004866876 -1.7084109 1.0563865 0.51628007
## 29: 0.004866876 -1.7084109 1.0563865 0.51628007
## 30: 0.004866876 -1.7084109 1.0563865 0.51628007
## 31: 0.004866876 -1.7084109 1.0563865 0.51628007
## 32: 0.004866876 -1.7084109 1.0563865 0.51628007
## 33: 0.004866876 -1.7084109 1.0563865 0.51628007
## 34: 0.004866876 -1.7084109 1.0563865 0.51628007
## 35: 0.004845179 -1.7779128 1.0925743 0.04880686
## 36: 0.004845179 -1.7779128 1.0925743 0.04880686
## 37: 0.004635436 -0.5796832 1.2128574 0.32603176
## 38: 0.004635436 -0.5796832 1.2128574 0.32603176
## 39: 0.004635436 -0.5796832 1.2128574 0.32603176
## 40: 0.005225222 -1.2149856 0.9031625 0.82402823
## 41: 0.005225222 -1.2149856 0.9031625 0.82402823
## 42: 0.005225222 -1.2149856 0.9031625 0.82402823
## 43: 0.005225222 -1.2149856 0.9031625 0.82402823
## 44: 0.005225222 -1.2149856 0.9031625 0.82402823
## 45: 0.005225222 -1.2149856 0.9031625 0.82402823
## 46: 0.005225222 -1.2149856 0.9031625 0.82402823
## 47: 0.005225222 -1.2149856 0.9031625 0.82402823
## 48: 0.005225222 -1.2149856 0.9031625 0.82402823
## 49: 0.005225222 -1.2149856 0.9031625 0.82402823
## 50: 0.005225222 -1.2149856 0.9031625 0.82402823
## 51: 0.005225222 -1.2149856 0.9031625 0.82402823
## 52: 0.005225222 -1.2149856 0.9031625 0.82402823
## 53: 0.005225222 -1.2149856 0.9031625 0.82402823
## 54: 0.005225222 -1.2149856 0.9031625 0.82402823
## 55: 0.005225222 -1.2149856 0.9031625 0.82402823
## 56: 0.005225222 -1.2149856 0.9031625 0.82402823
## 57: 0.005225222 -1.2149856 0.9031625 0.82402823
## 58: 0.005225222 -1.2149856 0.9031625 0.82402823
## 59: 0.005225222 -1.2149856 0.9031625 0.82402823
## 60: 0.004968046 -1.4394451 0.8949157 0.71371866
## 61: 0.004968046 -1.4394451 0.8949157 0.71371866
## 62: 0.004968046 -1.4394451 0.8949157 0.71371866
## 63: 0.004968046 -1.4394451 0.8949157 0.71371866
## 64: 0.004968046 -1.4394451 0.8949157 0.71371866
## 65: 0.004968046 -1.4394451 0.8949157 0.71371866
## 66: 0.004968046 -1.4394451 0.8949157 0.71371866
## 67: 0.004968046 -1.4394451 0.8949157 0.71371866
## 68: 0.004968046 -1.4394451 0.8949157 0.71371866
## 69: 0.004968046 -1.4394451 0.8949157 0.71371866
## 70: 0.004968046 -1.4394451 0.8949157 0.71371866
## 71: 0.004968046 -1.4394451 0.8949157 0.71371866
## 72: 0.004968046 -1.4394451 0.8949157 0.71371866
## 73: 0.005268284 -0.8383279 0.9900376 0.17121312
## 74: 0.005268284 -0.8383279 0.9900376 0.17121312
## 75: 0.005000790 -0.4703599 0.8714482 0.43210675
## 76: 0.005399375 -1.4831325 1.4450987 0.32741114
## 77: 0.004627003 -0.5983324 1.2383432 0.10503633
## 78: 0.004794327 -0.4644118 1.0058356 0.11286204
## 79: 0.004794327 -0.4644118 1.0058356 0.11286204
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF55" "ORF73" "ORF62"## [1] 5## [1] "ORF28" "ORF64_1" "ORF75"## [1] 3Remove genes from clusters ?
## [1] "ORF28" "ORF64_1" "ORF75"## [1] 3## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 6 20
## 2: 2 14
## 3: 7 13
## 4: 1 11
## 5: 3 9
## 6: 5 3
## 7: 4 2
## 8: 8 2
## 9: 12 2
## 10: 9 1
## 11: 10 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
